AMBER Archive (2009)

Subject: RE: [AMBER] Problem reading PDB file into XLEAP

From: Hopkins, Robert (
Date: Fri Mar 27 2009 - 17:09:11 CDT

Dear Dr. Case,

Thanks very much for your response and suggestions. The leaprc file
didn't need to be reloaded since I didn't exit/quit Xleap between
writing out/editing the IR_sol.pdb file and reloading it into Xleap.
My statement about the .prmtop and .inpcrd files should have been more
specific: although they appear to be normal, when I use them with the script (attached) and the following command:

sander -O -i -o IRsolmin.out -p IR_sol.prmtop -c
        -r IRsolmin.rst -ref IR_sol.inpcrd

the program 'hangs up'. I tried the same thing with tleap and got the
same result, even when I did *no* editing of the PDB file (i.e., wrote
out and read it right back in). I'll have to put in more time in trying
to use sleap since I haven't yet figured out how to easily source in all

the parameter files needed.

Although I've tried several approaches, so far I haven't yet seen a path
around the 'brick wall'. Thanks again.

Bob Hopkins


-----Original Message-----
From: [] On
Behalf Of David A. Case
Sent: Friday, March 27, 2009 7:39 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Problem reading PDB file into XLEAP

On Thu, Mar 26, 2009, Hopkins, Robert wrote:
> After I loaded a DNA file (DDIRinmin.pdb) into Xleap (Amber Tools 1.2)
> from Amber 9, it was solvated, counterions were added and a new PDB
> file (IR_sol.pdb) was created. I then edited the new file in order to
> remove the last water molecule from the file using Xemacs while
> the same file name. This edited file was then loaded into Xleap once
> again in order to create .prmtop and .inpcrd files, but none of the
> residues are being recognized in Xleap, as indicated in the leap.log.
> And, although .prmtop and .inpcrd files are created, these files do
> function properly when used with sander.

It looks like your leap.log file leaves out the beginning part of the
second leap run (with the modified pdb file)(?) I don't see where the
leaprc file is being processed.

You can ignore the "not found in name map" lines...I don't know why
these are still being printed.

I don't see any obvious problems with your files. I'd suggest trying it
again(!), and seeing what sleap does.


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